Release 0.5.0 [PR #22]

- New `__version__` in `__init__.py` should be automatically recognized in `setup.cfg`
- Refactoring into MVC/MVP started to enable new features (currently in awkward stage)
- NEW: select multiple samples to run (graphical interface still displays only one sample for now but all are selected)
- NEW: option to save/load protocols.

aurora/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.5.0"

aurora/engine/submit.py

@@ -16,7 +16,7 @@
 TomatoMonitorData = aiida.plugins.DataFactory('calcmonitor.monitor.tomatobiologic')
 TomatoMonitorCalcjob = aiida.plugins.CalculationFactory('calcmonitor.calcjob_monitor')
 
-MONITOR_CODE = load_code("monitor@localhost-verdi")
+#MONITOR_CODE = load_code("monitor@localhost-verdi")
 GROUP_SAMPLES = load_group("BatterySamples")
 GROUP_METHODS = load_group("CyclingSpecs")
 GROUP_CALCJOBS = load_group("CalcJobs")
@@ -41,7 +41,7 @@ def _find_job_remote_folder(job):
  return remote_folder
 
 def submit_experiment(sample, method, tomato_settings, monitor_job_settings, code_name,
- sample_node_label="", method_node_label="", calcjob_node_label=""):
+ sample_node_label="", method_node_label="", calcjob_node_label="", monitor_code=None):
  """
  sample : `aurora.schemas.battery.BatterySample`
  method : `aurora.schemas.cycling.ElectroChemSequence`
@@ -98,8 +98,11 @@ def submit_experiment(sample, method, tomato_settings, monitor_job_settings, cod
  monitor_protocol.store()
  monitor_protocol.label = "" # TODO? write default name generator - e.g "monitor-rate_600-cycles_2-thr_0.80"
 
+ if monitor_code is None:
+ monitor_code = load_code("monitor@localhost-verdi")
+
  monitor_builder = TomatoMonitorCalcjob.get_builder()
- monitor_builder.code = MONITOR_CODE
+ monitor_builder.code = monitor_code
  monitor_builder.metadata.options.parser_name = "calcmonitor.cycler"
  monitor_builder.monitor_protocols = {'monitor1': monitor_protocol}
 

aurora/interface/cycling/custom.py

@@ -3,13 +3,16 @@
 Cycling protocol customizable by the user.
 TODO: Enable the user to save a customized protocol.
 """
-
+import os
+import json
 import logging
 import ipywidgets as ipw
 import aurora.schemas.cycling
 from aurora.schemas.cycling import ElectroChemPayloads, ElectroChemSequence
 from .technique_widget import TechniqueParametersWidget
 
+from ipyfilechooser import FileChooser
+
 class CyclingCustom(ipw.VBox):
 
  BOX_STYLE = {'description_width': '25%'}
@@ -20,12 +23,19 @@ class CyclingCustom(ipw.VBox):
  BUTTON_STYLE = {'description_width': '30%'}
  BUTTON_LAYOUT = {'margin': '5px'}
  BUTTON_LAYOUT_2 = {'width': '20%', 'margin': '5px'}
+ #BUTTON_LAYOUT_3 = {'width': '43.5%', 'margin': '5px'}
+ BUTTON_LAYOUT_3 = {'width': '10%', 'margin': '5px'}
  GRID_LAYOUT = {"grid_template_columns": "30% 65%", 'width': '100%', 'margin': '5px'} # 'padding': '10px', 'border': 'solid 2px', 'max_height': '500px'
  DEFAULT_PROTOCOL = aurora.schemas.cycling.OpenCircuitVoltage
  _TECHNIQUES_OPTIONS = {f"{Technique.schema()['properties']['short_name']['default']} ({Technique.schema()['properties']['technique']['default']})": Technique
  for Technique in ElectroChemPayloads.__args__}
 
- def __init__(self, validate_callback_f):
+ def __init__(self, experiment_model, validate_callback_f):
+
+ if experiment_model is None:
+ raise ValueError('An experiment model must be provided.')
+ self.experiment_model = experiment_model
+ self.experiment_model.suscribe_observer(self)
 
  if not callable(validate_callback_f):
  raise TypeError("validate_callback_f should be a callable function")
@@ -37,8 +47,11 @@ def __init__(self, validate_callback_f):
  rows=10, value=None,
  description="",
  layout=self.BOX_LAYOUT)
+
+ self._update_protocol_steps_list_widget_options()
+
  self.w_button_add = ipw.Button(
- description="", button_style='info', tooltip="Add step", icon='plus',
+ description="", button_style='success', tooltip="Add step", icon='plus',
  style=self.BUTTON_STYLE, layout=self.BUTTON_LAYOUT_2)
  self.w_button_remove = ipw.Button(
  description="", button_style='danger', tooltip="Remove step", icon='minus',
@@ -50,9 +63,23 @@ def __init__(self, validate_callback_f):
  description="", button_style='', tooltip="Move step down", icon='arrow-down',
  style=self.BUTTON_STYLE, layout=self.BUTTON_LAYOUT_2)
 
+ self.w_button_load = ipw.Button(
+ description="Load", button_style='', tooltip="Load protocol", icon='',
+ style=self.BUTTON_STYLE, layout=self.BUTTON_LAYOUT_3)
+ self.w_button_save = ipw.Button(
+ description="Save", button_style='', tooltip="Save protocol", icon='',
+ style=self.BUTTON_STYLE, layout=self.BUTTON_LAYOUT_3)
+ home_directory = os.path.expanduser( '~' )
+ self.w_filepath_explorer = FileChooser(
+ home_directory, layout={'width': '70%', 'margin': '5px'},
+ )
+ self.w_filepath_explorer.default_path = home_directory
+ self.w_filepath_explorer.default_filename = 'saved_protocol.json'
+ self.w_filepath_explorer.reset()
+
  # initialize protocol steps list
- self._protocol_steps_list = ElectroChemSequence(method=[])
- self.add_protocol_step()
+ # self._protocol_steps_list = ElectroChemSequence(method=[])
+ # self.add_protocol_step()
 
  # initialize current step properties widget
  self.w_selected_step_technique_name = ipw.Dropdown(
@@ -82,11 +109,14 @@ def __init__(self, validate_callback_f):
  super().__init__()
  self.children = [
  self.w_header,
+ ipw.HBox([self.w_filepath_explorer, self.w_button_load, self.w_button_save]),
  self.w_protocol_label,
  ipw.GridBox([
  ipw.VBox([
  self.w_protocol_steps_list,
  ipw.HBox([self.w_button_add, self.w_button_remove, self.w_button_up, self.w_button_down]),
+ #ipw.HBox([self.w_button_load, self.w_button_save]),
+ #ipw.HBox([self.w_filepath_explorer]),
  ]),
  ipw.VBox([
  self.w_selected_step_technique_name,
@@ -102,11 +132,21 @@ def __init__(self, validate_callback_f):
  # setup automations
  ## steps list
  self.w_protocol_steps_list.observe(self._build_current_step_properties_widget, names='index')
- self.w_button_add.on_click(self.add_protocol_step)
- self.w_button_remove.on_click(self.remove_protocol_step)
- self.w_button_up.on_click(self.move_protocol_step_up)
- self.w_button_down.on_click(self.move_protocol_step_down)
 
+ #self.w_button_add.on_click(self.add_protocol_step)
+ #self.w_button_remove.on_click(self.remove_protocol_step)
+ #self.w_button_up.on_click(self.move_protocol_step_up)
+ #self.w_button_down.on_click(self.move_protocol_step_down)
+
+ self.w_button_add.on_click(self.w_button_add_click)
+ self.w_button_remove.on_click(self.w_button_remove_click)
+ self.w_button_up.on_click(self.w_button_up_click)
+ self.w_button_down.on_click(self.w_button_down_click)
+
+ self.w_button_load.on_click(self.button_load_protocol_click)
+ self.w_button_save.on_click(self.button_save_protocol_click)
+
+
  ## current step's properties:
  ### if technique type changes, we need to initialize a new technique from scratch the widget observer may detect a change
  ### even when a new step is selected therefore we check whether the new technique is the same as the one stored in
@@ -118,32 +158,46 @@ def __init__(self, validate_callback_f):
  ### validate protocol
  self.w_validate.on_click(lambda arg: self.callback_call(validate_callback_f))
 
+ def update(self):
+ """Receive updates from the model"""
+ self._update_protocol_steps_list_widget_options()
+ self._build_current_step_properties_widget()
+ # Automatically done by _build_current_step_properties_widget
+ #self._build_technique_parameters_widgets()
+
  @property
  def protocol_steps_list(self):
  "The list of steps composing the cycling protocol. Each step must be one of the allowed ElectroChemPayloads."
- return self._protocol_steps_list
+ return self.experiment_model.selected_protocol
+ #return self._protocol_steps_list
 
  @property
  def selected_step_technique(self):
  "The step that is currently selected."
- return self.protocol_steps_list.method[self.w_protocol_steps_list.index]
+ return self.experiment_model.selected_protocol.method[self.w_protocol_steps_list.index]
+ #return self.protocol_steps_list.method[self.w_protocol_steps_list.index]
 
  @selected_step_technique.setter
  def selected_step_technique(self, technique):
- self.protocol_steps_list.method[self.w_protocol_steps_list.index] = technique
+ self.experiment_model.selected_protocol.method[self.w_protocol_steps_list.index] = technique
+ #self.protocol_steps_list.method[self.w_protocol_steps_list.index] = technique
 
  def _count_technique_occurencies(self, technique):
- return [type(step) for step in self.protocol_steps_list.method].count(technique)
+ return [type(step) for step in self.experiment_model.selected_protocol.method].count(technique)
+ #return [type(step) for step in self.protocol_steps_list.method].count(technique)
 
  def _update_protocol_steps_list_widget_options(self, new_index=None):
  old_selected_index = self.w_protocol_steps_list.index
- self.w_protocol_steps_list.options = [f"[{idx + 1}] - {step.name}" for idx, step in enumerate(self.protocol_steps_list.method)]
+ self.w_protocol_steps_list.options = [f"[{idx + 1}] - {step.name}" for idx, step in enumerate(self.experiment_model.selected_protocol.method)]
+ #self.w_protocol_steps_list.options = [f"[{idx + 1}] - {step.name}" for idx, step in enumerate(self.protocol_steps_list.method)]
  if new_index is not None:
  old_selected_index = new_index
  if (old_selected_index is None) or (old_selected_index < 0):
  self.w_protocol_steps_list.index = 0
- elif old_selected_index >= self.protocol_steps_list.n_steps:
- self.w_protocol_steps_list.index = self.protocol_steps_list.n_steps - 1
+ elif old_selected_index >= self.experiment_model.selected_protocol.n_steps:
+ self.w_protocol_steps_list.index = self.experiment_model.selected_protocol.n_steps - 1
+ #elif old_selected_index >= self.protocol_steps_list.n_steps:
+ # self.w_protocol_steps_list.index = self.protocol_steps_list.n_steps - 1
  else:
  self.w_protocol_steps_list.index = old_selected_index
 
@@ -153,19 +207,24 @@ def DEFAULT_STEP_NAME(self, technique):
  def add_protocol_step(self, dummy=None):
  name = self.DEFAULT_STEP_NAME(self.DEFAULT_PROTOCOL)
  logging.debug(f"Adding protocol step {name}")
- self.protocol_steps_list.add_step(self.DEFAULT_PROTOCOL(name=name))
- self._update_protocol_steps_list_widget_options(new_index=self.protocol_steps_list.n_steps-1)
+ self.experiment_model.selected_protocol.add_step(self.DEFAULT_PROTOCOL(name=name))
+ self._update_protocol_steps_list_widget_options(new_index=self.experiment_model.selected_protocol.n_steps-1)
+ #self.protocol_steps_list.add_step(self.DEFAULT_PROTOCOL(name=name))
+ #self._update_protocol_steps_list_widget_options(new_index=self.protocol_steps_list.n_steps-1)
 
  def remove_protocol_step(self, dummy=None):
- self.protocol_steps_list.remove_step(self.w_protocol_steps_list.index)
+ self.experiment_model.selected_protocol.remove_step(self.w_protocol_steps_list.index)
+ #self.protocol_steps_list.remove_step(self.w_protocol_steps_list.index)
  self._update_protocol_steps_list_widget_options()
 
  def move_protocol_step_up(self, dummy=None):
- self.protocol_steps_list.move_step_backward(self.w_protocol_steps_list.index)
+ self.experiment_model.selected_protocol.move_step_backward(self.w_protocol_steps_list.index)
+ #self.protocol_steps_list.move_step_backward(self.w_protocol_steps_list.index)
  self._update_protocol_steps_list_widget_options(new_index=self.w_protocol_steps_list.index - 1)
 
  def move_protocol_step_down(self, dummy=None):
- moved = self.protocol_steps_list.move_step_forward(self.w_protocol_steps_list.index)
+ moved = self.experiment_model.selected_protocol.move_step_forward(self.w_protocol_steps_list.index)
+ #moved = self.protocol_steps_list.move_step_forward(self.w_protocol_steps_list.index)
  self._update_protocol_steps_list_widget_options(new_index=self.w_protocol_steps_list.index + 1)
 
  ## SELECTED STEP METHODS
@@ -211,4 +270,50 @@ def discard_current_step_properties(self, dummy=None):
 
  def callback_call(self, callback_function):
  "Call a callback function and this class instance to it."
- return callback_function(self)
+ return callback_function(self)
+
+
+ ################################################################################
+ # NEW DESIGN
+ ################################################################################
+ # TODO: figure out what the b param is
+
+ def w_button_add_click(self, b):
+ """Click event for w_button_add"""
+ self.experiment_model.add_protocol_step()
+ number_of_steps = self.experiment_model.selected_protocol.n_steps
+ self._update_protocol_steps_list_widget_options(new_index = number_of_steps - 1)
+
+ def w_button_remove_click(self, b):
+ """Click event for w_button_remove"""
+ self.experiment_model.remove_protocol_step(self.w_protocol_steps_list.index)
+
+ def w_button_up_click(self, b):
+ """Click event for w_button_up"""
+ # TODO I need to add a guard on the index?
+ current_index = self.w_protocol_steps_list.index
+ self.experiment_model.move_protocol_step_up(current_index)
+ self._update_protocol_steps_list_widget_options(new_index = current_index - 1)
+
+ def w_button_down_click(self, b):
+ """Click event for w_button_down"""
+ # TODO I need to add a guard on the index?
+ current_index = self.w_protocol_steps_list.index
+ self.experiment_model.move_protocol_step_down(current_index)
+ self._update_protocol_steps_list_widget_options(new_index = current_index + 1)
+
+ def button_load_protocol_click(self, dummy=None):
+ """Loads the protocol from a file."""
+ #filepath = '/home/aiida/saved_protocol.json'
+ filepath = self.w_filepath_explorer.selected
+ if filepath is None:
+ return
+ self.experiment_model.load_protocol(filepath)
+
+ def button_save_protocol_click(self, dummy=None):
+ """Saves the protocol from a file."""
+ filepath = self.w_filepath_explorer.selected
+ if filepath is None:
+ return
+ self.experiment_model.save_protocol(filepath)
+

aurora/interface/cycling/technique_widget.py

@@ -23,7 +23,8 @@ def build_parameter_widget(param_obj):
  w_check = ipw.Checkbox(
  value=param_obj.required or (param_obj.value is not None),
  disabled=param_obj.required,
- description='', style=CHECKBOX_STYLE, layout=CHECKBOX_LAYOUT)
+ description='', style=CHECKBOX_STYLE, layout=CHECKBOX_LAYOUT
+ )
 
  # read the value of parameter. If None, take use the default value
  param_value = param_obj.value if param_obj.value is not None else param_obj.default_value